I followed the steps but charged it in my computer for the night. Now I switched it back on and it says low battery.
Maybe my computer didn't charge it.
Do you think it's okay that I turned it on? Have I damaged anything?

I am thinking of charging it with the wall charger overnight and only then switch it back on. Do you think it will solve the problem?
Or should I undo the root, fully charge it and then root again and delete the battery file?

Maybe the root image and/or rescue image contain data of a not fully charged battery? Who knows in what state the Reader has been when the developer backed up the system? Even worse, if that's true, you can't re-initialize the rescue image's battery data because you don't have android access.

The root set is not based on a disk image (mostly just some files that are added), but the restore set is, so indeed there could be a problem there. Probably best if that battery file were just removed from it. Simple enough if you have a working Linux system, otherwise a bit more difficult.

I think that I looked at the first, so that I could replicate what it did from NetBSD (which is my preferred OS).
The second, I sometimes use that for testing.
But I do have a dual boot including Linux on my laptop, so I have a Xubuntu on hand when I need it.